EMP can arc through shields depending on the hard flux of the target at listed percentage rate on a given weapon, I think. There's weapon health which I believe is fixed based on the size of the mount (though I don't remember the exact health values), and then there's EMP damage which is set for any weapon as well as listed in-game. EMP damage ignores the armor of the target to damage weapons and engines (which other weapons have to go through before damaging weapons and engines), unlike more conventional fire, which is the reason why it knocks out those systems so easily. The EMP effect occurs around the point of impact, if the bit above didn't make that obvious. There's also EMP arcing when it hits the surface of the target, which I think can arc to other parts of a ship and affect those areas, though that was added (relatively) recently so I couldn't tell you much on that. I think *some* EMP weapons also have the ability to briefly overload a ship when it makes contact with the hull, though I think the only weapon currently capable of doing consistently is the Tachyon Lance, though the Ion Cannon might also have a small chance (but I don't remember all the patchnotes).
All you really need to know to use EMP weapons effectively is that you have to target weapons and engines and, the higher the hard flux of a ship, the better chance EMP will have of arcing through and disabling systems regardless.